Seed banking is an invaluable tool in plant conservation, both as an archive and a source of genetic variation. Despite the increasing focus on the validation of sampling strategies, few studies have empirically related diversity in seed bank collections with variation in wild-provenance populations. By using a set of nuclear microsatellites, we investigated genetic diversity in British populations of Taxus baccata (European yew tree). We used our findings as a baseline for the quantification of genetic diversity captured in the germplasm collections maintained by the Millennium Seed Bank (Royal Botanic Gardens, Kew), in terms of allelic richness and allelic capture. We observed that genetic differentiation in wild populations of yew is compatible with highly effective gene flow, with no geographic patterns. Heterozygosity is lower than expected for a dioecious obligate outbreeder. Seed collections are representative of wild populations in terms of allelic capture, including rare and locally common variants, indicating that the current sampling protocol implemented by the UK National Tree Seed Project is appropriate. Specific sampling strategies might be improved by including more populations at the edge of the range and in remote localities, even at the expense of contiguous populations. Our methods may be applied to evaluate allelic capture in other germplasm collections for which a baseline exists, i.e. in which genetic diversity in the wild-provenance populations is known. Our recommendations related to sampling strategies can be extended to other tree species with continuous distributions and effective gene flow.